Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101571
Name   oriT_pMFDS1013836 in_silico
Organism   Escherichia coli strain MFDS1013836
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JAQMUU010000004 (5042..5165 [+], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 41..48, 61..68  (AAAAACAA..TTGTTTTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_pMFDS1013836
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGTTTTTTTAATCATTAGTTTATGTTCTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1393 GenBank   WP_064578954
Name   traI_V6M02_RS27885_pMFDS1013836 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192244.09 Da        Isoelectric Point: 5.9188

>WP_064578954.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGRNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIEAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERVRAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMIAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYETEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVELPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGRTEQAVREIAGQERERAVTSEREAALPESVLREPQREREAVREVVRENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(575-626)

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)


  Protein structure



No available structure.




Auxiliary protein

ID   521 GenBank   WP_040073112
Name   WP_040073112_pMFDS1013836 insolico UniProt ID   _
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14556.62 Da        Isoelectric Point: 5.0278

>WP_040073112.1 conjugal transfer relaxosome DNA-binding protein TraM [Escherichia coli]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSIEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure



No available structure.



ID   522 GenBank   WP_001254386
Name   WP_001254386_pMFDS1013836 insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5


T4CP

ID   1033 GenBank   WP_001064245
Name   traC_V6M02_RS27780_pMFDS1013836 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99159.81 Da        Isoelectric Point: 5.8486

>WP_001064245.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

  Protein structure



No available structure.



ID   1034 GenBank   WP_062873762
Name   traD_V6M02_RS27870_pMFDS1013836 insolico UniProt ID   _
Length   717 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 81434.90 Da        Isoelectric Point: 5.0485

>WP_062873762.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAASLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPDMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQRREEVN
INVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 4470..30607

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V6M02_RS27655 1..382 + 382 Protein_0 hypothetical protein -
V6M02_RS27660 437..871 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
V6M02_RS27665 868..1630 + 763 Protein_2 plasmid SOS inhibition protein A -
V6M02_RS27670 1599..1787 - 189 WP_032084246 hypothetical protein -
V6M02_RS27675 1809..1958 + 150 Protein_4 plasmid maintenance protein Mok -
V6M02_RS27680 1900..2025 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
V6M02_RS27685 2245..2475 + 231 WP_074014914 hypothetical protein -
V6M02_RS27690 2473..2646 - 174 Protein_7 hypothetical protein -
V6M02_RS27695 2716..2922 + 207 WP_000547968 hypothetical protein -
V6M02_RS27700 2947..3233 + 287 Protein_9 hypothetical protein -
V6M02_RS27705 3352..4173 + 822 WP_074014913 DUF932 domain-containing protein -
V6M02_RS27710 4470..5117 - 648 WP_123007297 transglycosylase SLT domain-containing protein virB1
V6M02_RS27715 5394..5777 + 384 WP_040073112 conjugal transfer relaxosome DNA-binding protein TraM -
V6M02_RS27720 5967..6653 + 687 WP_000332492 PAS domain-containing protein -
V6M02_RS27725 6747..6974 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
V6M02_RS27730 7008..7373 + 366 WP_000340270 type IV conjugative transfer system pilin TraA -
V6M02_RS27735 7388..7699 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
V6M02_RS27740 7721..8287 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
V6M02_RS27745 8274..9001 + 728 Protein_18 type-F conjugative transfer system secretin TraK -
V6M02_RS27750 9001..10428 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
V6M02_RS27755 10418..11008 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
V6M02_RS27760 10995..11192 + 198 WP_001324648 conjugal transfer protein TrbD -
V6M02_RS27765 11204..11454 + 251 Protein_22 conjugal transfer protein TrbG -
V6M02_RS27770 11451..11966 + 516 WP_332829757 type IV conjugative transfer system lipoprotein TraV traV
V6M02_RS27775 12101..12322 + 222 WP_001278689 conjugal transfer protein TraR -
V6M02_RS27780 12482..15109 + 2628 WP_001064245 type IV secretion system protein TraC virb4
V6M02_RS27785 15106..15492 + 387 WP_032082946 type-F conjugative transfer system protein TrbI -
V6M02_RS27790 15489..16121 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
V6M02_RS27795 16118..17110 + 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
V6M02_RS27800 17119..17757 + 639 WP_000777695 type-F conjugative transfer system pilin assembly protein TrbC trbC
V6M02_RS27805 17754..19562 + 1809 WP_032082947 type-F conjugative transfer system mating-pair stabilization protein TraN traN
V6M02_RS27810 19589..19846 + 258 WP_000864318 conjugal transfer protein TrbE -
V6M02_RS27815 19839..20582 + 744 WP_032082948 type-F conjugative transfer system pilin assembly protein TraF traF
V6M02_RS27820 20598..20945 + 348 WP_115429732 conjugal transfer protein TrbA -
V6M02_RS27825 20947..21222 - 276 WP_001513501 hypothetical protein -
V6M02_RS27830 21303..21587 + 285 WP_000624108 type-F conjugative transfer system pilin chaperone TraQ -
V6M02_RS27835 21574..22119 + 546 WP_032082911 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
V6M02_RS27840 22049..22390 + 342 WP_001442101 P-type conjugative transfer protein TrbJ -
V6M02_RS27845 22377..22769 + 393 WP_032082924 F-type conjugal transfer protein TrbF -
V6M02_RS27850 22756..24129 + 1374 WP_000944319 conjugal transfer pilus assembly protein TraH traH
V6M02_RS27855 24126..26951 + 2826 WP_032082912 conjugal transfer mating-pair stabilization protein TraG traG
V6M02_RS27860 26948..27457 + 510 WP_032082913 conjugal transfer entry exclusion protein TraS -
V6M02_RS27865 27471..28202 + 732 WP_024187508 conjugal transfer complement resistance protein TraT -
V6M02_RS27870 28454..30607 + 2154 WP_062873762 type IV conjugative transfer system coupling protein TraD virb4
V6M02_RS27875 30616..31014 - 399 WP_000911317 type II toxin-antitoxin system VapC family toxin -
V6M02_RS27880 31014..31241 - 228 WP_000450532 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   2015 GenBank   NZ_JAQMUU010000004
Plasmid name   pMFDS1013836 Incompatibility group   IncFII
Plasmid size   101631 bp Coordinate of oriT [Strand]   5042..5165 [+]
Host baterium   Escherichia coli strain MFDS1013836

Cargo genes

Drug resistance gene   -
Virulence gene   estIa
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -